Related papers: Improving sequencing by tunneling with multiplexin…
Rapid and cost-effective DNA sequencing at the single nucleotide level might be achieved by measuring a transverse electronic current as single-stranded DNA is pulled through a nano-sized pore. In order to enhance the electronic coupling…
Nanopore based sequencing has demonstrated significant potential for the development of fast, accurate, and cost-efficient fingerprinting techniques for next generation molecular detection and sequencing. We propose a specific multi-layered…
We suggest to discriminate single DNA bases via transverse ionic transport, namely by detecting the ionic current that flows in a channel while a single-stranded DNA is driven through an intersecting nanochannel. Our all-atom molecular…
A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of…
We review recent advances in the DNA sequencing based on the measurement of transverse electrical currents. Device configurations proposed in the literature are classified according to whether the molecular fingerprints appear as the major…
The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4]…
In shotgun sequencing, the input string (typically, a long DNA sequence composed of nucleotide bases) is sequenced as multiple overlapping fragments of much shorter lengths (called \textit{reads}). Modelling the shotgun sequencing pipeline…
Previous theoretical studies have shown that measuring the transverse current across DNA strands while they translocate through a nanopore or channel may provide a statistically distinguishable signature of the DNA bases, and may thus allow…
We propose using graphene electrodes with hydrogenated edges for solid-state nanopore-based DNA sequencing, and perform molecular dynamics simulations in conjunction with electronic transport calculations to explore the potential merits of…
Rapid sequencing of individual human genome is prerequisite to genomic medicine, where diseases will be prevented by preemptive cures. Quantum-mechanical tunneling through single-stranded DNA in a solid-state nanopore has been proposed for…
Nanopore sequencing is an emerging new technology for sequencing DNA, which can read long fragments of DNA (~50,000 bases) in contrast to most current short-read sequencing technologies which can only read hundreds of bases. While nanopore…
{\it De novo} protein sequencing is essential for understanding cellular processes that govern the function of living organisms and all post-translational events and other sequence modifications that occur after a protein has been…
The emerging field of DNA storage employs strands of DNA bases (A/T/C/G) as a storage medium for digital information to enable massive density and durability. The DNA storage pipeline includes: (1) encoding the raw data into sequences of…
Fast, reliable and inexpensive DNA sequencing is an important pursuit in healthcare, especially in personalized medicine with possible deep societal impacts. Despite significant progress of various nanopore-based sequencing configurations,…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
Translocation of DNA through a nanopore with embedded electrodes is at the centre of new rapid inexpensive sequencing methods which allow distinguishing the four nucleobases by their different electronic structure. However, the subnanometer…
We propose a DNA sequencing scheme based on silicene nanopores. Using first principles theory, we compute the electrical properties of such pores in the absence and presence of nucleobases. Within a two-terminal geometry, we analyze the…
We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…
The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes…
We develop statistically based methods to detect single nucleotide DNA mutations in next generation sequencing data. Sequencing generates counts of the number of times each base was observed at hundreds of thousands to billions of genome…